I think you're going to need to wait for her to come to you. Which is a sucky process but you did shitty things and need to deal with the consequences of those actions. One of which is Skye hating you.
You live your life. You figure out what you're gonna do around here or whatever and you give her time and space and maybe when she's ready she'll decide to speak to you. Maybe she won't ever want to and you'll have to live with that.